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knitr::opts_chunk$set(fig.width = 6, fig.height = 4, fig.path = 'Figs/',
                      echo = FALSE, message = FALSE, warning = FALSE)

dir_git     <- path.expand('~/github/ohibc')
source(file.path(dir_git, 'src/R/common.R'))  
dir_spatial <- file.path(dir_git, 'prep/_spatial')  
dir_anx     <- file.path(dir_M, 'git-annex/bcprep')


### goal specific folders and info
goal      <- 'fis'
scenario  <- 'v2017'
dir_goal  <- file.path(dir_git, 'prep', goal, scenario)
dir_goal_anx <- file.path(dir_anx, goal, scenario)

### provenance tracking
library(provRmd); prov_setup()

### Kobe plot functions
source(file.path(dir_goal, 'kobe_fxns.R'))

### set up proj4string options: BC Albers and WGS84
p4s_wgs84 <- '+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0'
p4s_bcalb <- '+proj=aea +lat_1=50 +lat_2=58.5 +lat_0=45 +lon_0=-126 +x_0=1000000 +y_0=0 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0'

1 Summary

Process RAM database for British Columbia fisheries stock status and harvest levels. Each RAM stock will be filtered to the RAM stock ID and RAM area (to separate region-specific stocks), and then the stock status parameters B/Bmsy and F/Fmsy for that stock for each year reported.

Total catch data for each stock for each year will be used to determine final weightings. Since the distribution of catch data is not differentiated within the reporting region, we will use SAUP and/or DFO spatial catch data to determine the distribution and allocate the total catch proportionally.


2 Data Source

Reference: RAM

Downloaded: 2016

Description: Fishery status (B/Bmsy and F/Fmsy) for stocks in BC waters

Time range: 1927-2015 (varies by stock)

Format: .RData file


3 Methods

Explore RAM: Preliminary RAM database v. 3.8. Load from .RData file, including time series and metadata. This initial chunk explores the variables included in the data.

3.1 BC-specific stocks

From global RAM data, filter to northeastern Pacific stocks whose assessment is by Canada or multinational bodies. Of these, select parameters that match ‘BdivBmsy*’, ‘FdivFmsy*’, ‘UdivUmsy*’, ‘Ctouse*’. Note that this excludes salmon species from this portion of the assessment.

3.1.0.1 Salmon stocks with available parameters:

3.1.0.2 Fish stocks represented in this dataset, including span of years and number of missing years in the series:

3.1.1 Examine time series of stocks

For each BC-specific stock, determine time series of B/Bmsy, F/Fmsy, and catch.

3.2 Plot stock status against modified Kobe

3.3 Associate stocks with spatial boundaries

Spatial boundaries for RAM stocks are derived from shapefiles provided by DFO.

  • From dfo_khunter/d2017/boundaries.gdb:
    • QCI aka Haida Gwaii, WCVANI, QCS, SoG, CC
  • From dfo_khunter/d2017/shrimp_trawl_areas/DFO_BC_SHRIMP_TRAWL_MGMT_AREA.shp:
    • SMA-14, SMA-FR, SMA-PRD
  • From dfo_khunter/d2016/management_boundaries/groundfish_mgmt_areas/MajorMinor_GroundfishManagementAreas.shp:
    • 5AB
  • BCW and PCOAST are union of all (areas 1-5) from boundaries.gdb
  • WCVANI-SOG-QCI is the union of those areas (1, 4, 5)
  • HS will be the area between Haida Gwaii island and the North Coast, bounded on the south by Area 5AB and bounded on the north at the level of the northeastern-most point of Haida Gwaii

FRDU is Fraser River Designatable Unit - since eulachon are harvested when they return to the mouth of the Fraser River, we will assume that this fishery falls entirely within Strait of Georgia region. If SAUP data are available, perhaps we can use those instead.

## OGR data source with driver: ESRI Shapefile 
## Source: "/home/shares/ohi/git-annex/bcprep/fis/v2017/stock_boundaries", layer: "stock_boundaries_bcalb"
## with 10 features
## It has 2 fields

4 Provenance

  • Run ID: 11 (977d61c); run tag: “standard run”
  • Run elapsed time: 83.286 seconds; run memory usage: 26810.6 MB
  • System info:
    • System: Linux, Release: 4.4.0-57-generic. Machine: x86_64. User: ohara.
    • R version: R version 3.4.0 (2017-04-21), Platform: x86_64-pc-linux-gnu, Running under: Ubuntu 14.04.5 LTS.
    • Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base
    • Other attached packages: provRmd_0.1.1, stringr_1.2.0, RColorBrewer_1.1-2, dplyr_0.5.0, purrr_0.2.2, readr_1.1.0, tidyr_0.6.2, tibble_1.3.3, ggplot2_2.2.1.9000, tidyverse_1.1.1
%3 13 kobe_fxns.R 14 DBdata.RData 3 data_prep_fis_ram.Rmd#bc_specific 14->3 used 15 bc_stocks_ram.csv 2 data_prep_fis_ram.Rmd#attach_timeseries_data 15->2 used 6 data_prep_fis_ram.Rmd#examine_salmon_timeseries_data 15->6 used 16 bc_stocks_ts_ram.csv 4 data_prep_fis_ram.Rmd#create_list_of_spp 16->4 used 12 data_prep_fis_ram.Rmd#stocks_b_bmsy_f_fmsy 16->12 used 17 ram_ids_to_names_raw.csv 18 ram_b_bmsy.csv 9 data_prep_fis_ram.Rmd#plot_stock_timeseries 18->9 used 5 data_prep_fis_ram.Rmd#examine_each_stock 18->5 used 7 data_prep_fis_ram.Rmd#get_dfo_boundary_info 18->7 used 19 ram_f_fmsy.csv 19->9 used 19->5 used 20 ram_catch.csv 20->9 used 21 ram_ids_to_names.csv 21->9 used 21->5 used 22 ram_stock_id_spans.png 23 kobe_bocaccio_bc_all.png 24 kobe_pacific_ocean_perch_qci.png 25 kobe_pacific_ocean_perch_wcvani.png 26 kobe_english_sole_hecate_strait.png 27 kobe_canary_rockfish_wcvani-sog-qci.png 28 kobe_rock_sole_qcs.png 29 kobe_rock_sole_hecate_strait.png 30 kobe_pacific_herring_cc.png 31 kobe_pacific_herring_qci.png 32 kobe_pacific_herring_sog.png 33 kobe_pacific_herring_wcvani.png 34 kobe_lingcod_sog.png 35 kobe_swordfish_e_pac.png 36 kobe_swordfish_n_pac.png 37 kobe_pacific_bluefin_tuna.png 38 kobe_pacific_cod_qcs.png 39 kobe_pacific_cod_hecate_strait.png 40 kobe_pacific_cod_wcvani.png 41 kobe_sablefish_bc_all.png 42 kobe_albacore_tuna_n_pac.png 43 kobe_blue_marlin_pac.png 44 kobe_bigeye_tuna_e_pac.png 45 kobe_yellowfin_tuna_e_pac.png 46 kobe_northern_shrimp_sma_fr.png 47 kobe_northern_shrimp_sma_prd.png 48 kobe_sidestripe_shrimp_sma_prd.png 49 kobe_sidestripe_shrimp_sma_fr.png 50 kobe_northern_shrimp_sma_14.png 51 kobe_sidestripe_shrimp_sma_14.png 52 kobe_eulachon_fraser_river_du.png 53 ram_area_ids.csv 53->7 used 54 ram_stock_to_area.csv 55 ohibc_rgn_to_ram_area.csv 1 data_prep_fis_ram.Rmd 11 data_prep_fis_ram.Rmd#setup 1->11 wasExecutedBy 1->3 wasExecutedBy 1->2 wasExecutedBy 1->6 wasExecutedBy 1->4 wasExecutedBy 1->12 wasExecutedBy 1->9 wasExecutedBy 1->5 wasExecutedBy 1->7 wasExecutedBy 8 data_prep_fis_ram.Rmd#match_dfo_areas_to_ohibc_rgns 1->8 wasExecutedBy 10 data_prep_fis_ram.Rmd#provenance 1->10 wasExecutedBy 11->13 wasExecutedBy 3->15 wasGeneratedBy 2->16 wasGeneratedBy 4->17 wasGeneratedBy 12->18 wasGeneratedBy 12->19 wasGeneratedBy 12->20 wasGeneratedBy 9->22 wasGeneratedBy 5->23 wasGeneratedBy 5->24 wasGeneratedBy 5->25 wasGeneratedBy 5->26 wasGeneratedBy 5->27 wasGeneratedBy 5->28 wasGeneratedBy 5->29 wasGeneratedBy 5->30 wasGeneratedBy 5->31 wasGeneratedBy 5->32 wasGeneratedBy 5->33 wasGeneratedBy 5->34 wasGeneratedBy 5->35 wasGeneratedBy 5->36 wasGeneratedBy 5->37 wasGeneratedBy 5->38 wasGeneratedBy 5->39 wasGeneratedBy 5->40 wasGeneratedBy 5->41 wasGeneratedBy 5->42 wasGeneratedBy 5->43 wasGeneratedBy 5->44 wasGeneratedBy 5->45 wasGeneratedBy 5->46 wasGeneratedBy 5->47 wasGeneratedBy 5->48 wasGeneratedBy 5->49 wasGeneratedBy 5->50 wasGeneratedBy 5->51 wasGeneratedBy 5->52 wasGeneratedBy 7->54 wasGeneratedBy 8->55 wasGeneratedBy